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- PDB-1n5x: Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n5x | ||||||
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Title | Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound | ||||||
![]() | Xanthine Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Molybdopterin / TEI-6720 / Flavoprotein / FAD / Iron-Sulfur Center / Fe2/S2 Center | ||||||
Function / homology | ![]() xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding ...xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okamoto, K. / Eger, B.T. / Nishino, T. / Kondo, S. / Pai, E.F. / Nishino, T. | ||||||
![]() | ![]() Title: An Extremely Potent Inhibitor of Xanthine Oxidoreductase: Crystal Structure of the Enzyme-Inhibitor Complex and Mechanism of Inhibition Authors: Okamoto, K. / Eger, B.T. / Nishino, T. / Kondo, S. / Pai, E.F. / Nishino, T. #1: ![]() Title: Hypouricemic effect of the novel xanthine oxidase inhibitor, TEI-6720, in rodents Authors: Osada, Y. / Tsuchimoto, M. / Fukushima, H. / Takahashi, K. / Kondo, S. / Hasegawa, M. / Komoriya, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 449.3 KB | Display | ![]() |
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PDB format | ![]() | 350.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762 KB | Display | ![]() |
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Full document | ![]() | 849.3 KB | Display | |
Data in XML | ![]() | 61.1 KB | Display | |
Data in CIF | ![]() | 87.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fo4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 146861.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 12 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/TEI.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/TEI.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: batch slide Details: PEG4000, DTT, Glycerol, Batch Slide, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 22, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 78047 / Num. obs: 74031 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.24 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 9.59 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.17 / Num. unique all: 3646 / Rsym value: 0.442 / % possible all: 98.2 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.116 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1FO4 Resolution: 2.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: STRICT NCS WAS USED THROUGHOUT
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Displacement parameters | Biso mean: 21 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT NCS | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.85 Å / Rfactor Rfree error: 0.038
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor obs: 0.244 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å |